On formation‐based sampling proxies and why they should not be used to correct the fossil record

The fossil record is a unique resource on the history of life, but it is well known to be incomplete. In a series of high‐profile papers, a residual modelling technique has been applied to correct the raw palaeodiversity signal for this bias and incompleteness, and the claim is made that the processed time series are more accurate than the raw data. We apply empirical and simulation approaches to test for correlation and directionality of any relationships between rock and fossil data. The empirical data comprise samples of the global fossil record through the Phanerozoic, and we use simulations to assess whether randomly sampled subsets of modelled data can be improved by application of the residual modelling technique. Our results show that using formation counts as a sampling proxy to correct the fossil record via residual modelling is ill founded. The supposedly independent model of sampling is information‐redundant with respect to the raw palaeodiversity data it seeks to correct, and so the outputs are generally likely to be further from the truth than the raw data. We recommend that students of palaeodiversity cease to use residual modelling estimates based on formation counts, and suggest that results from a substantial number of papers published in the past ten years require re‐evaluation.     

Thresholds of potential concern as benchmarks in the management of African savannahs

In the Kruger National Park (KNP), South Africa, ecosystem managers use a series of monitoring endpoints, known as thresholds of potential concern (TPCs), to define the upper and the lower levels of accepted variation in ecosystems. For woody vegetation, the current TPC suggests that woody cover should not drop by more than 80% of its 'highest ever' value. In this paper, we explore the utility of palaeoecological data in informing TPCs. We use calibrated fossil pollen data to explore variability in vegetation at two sites over the past 5000 years, to provide a long-term record of changes in woody vegetation cover and a context for interpreting more recent vegetation change. The fossil pollen data are calibrated using studies of modern pollen and vegetation from KNP; arboreal pollen percentage was simulated using pollen-landscape modelling software for savannah landscapes of varying woody vegetation cover, and the relationship between vegetation and pollen data was quantified using nonlinear regression. This quadratic equation was then applied to fossil pollen data in order to estimate woody vegetation cover from arboreal pollen percentages. Our results suggest that the TPCs have not been exceeded during the period represented in the pollen record, because estimated woody vegetation cover has remained above 20% of its highest ever value. By comparing the fossil pollen data with TPCs, our study demonstrates how palaeoecological data can be presented in a form that is directly relevant to management objectives.     

Changes in land plant function over the Phanerozoic: reconstructions based on the fossil record

Major fluctuations in the concentrations of atmospheric CO₂ and O₂, are predicted by historical long-term carbon and oxygen cycle models of atmospheric evolution and will have impacted directly on past climates, plant function and evolutionary processes. Here, palaeobotanical evidence is presented from the stomatal density record of fossil leaves spanning the past 400 Myr supporting the predicted changes in atsmopheric CO₂. Evidence from experiments on plants exposed to long-term high CO₂, environments and the newly-assembled fossil data indicate the potential for genetic modification of stomatal characters. The influence of the changes in fossil stomatal characteristics and atmospheric composition on the rates of leaf gas exchange over the course of land plant evolution has been investigated through modelling. Three contrasting eras of plain water economics emerge in the Devonian (high), Carboniferous (low) and from the Upper Jurassic to the present-day (high but declining). These patterns of change result from structural changes of the leaves and the impact of atmospheric CO₂, and O₂, concentrations on RuBisCo function and are consistent with the fossil evidence of sequential appearances of novel plant anatomical changes. The modelling approach is tested by comparing predicted leaf stable carbon isotope ratios with those measured on fossil plant and organic material. Viewed in a geological context, current and future increases in the concentration of atmospheric CO₂, might be considered as restoring plant function to that more typically experienced by plants over the majority of their evolutionary history.     

Past tree range dynamics in the Iberian Peninsula inferred through phylogeography and palaeodistribution modelling: A review

The forests in the Iberian Peninsula have been strongly influenced by past climatic changes, but reconstructing their historical distributions and dynamics is very difficult due to the complex climatic characteristics and relief of the region. Research disciplines such as phylogeography and species distribution modelling can describe the past range dynamics of individual tree species in relatively great detail and help elucidate how these species have reacted to climatic changes. Here we review phylogeographical and modelling studies from species representative of the major Iberian forest types and attempt to extract general trends from the diversity of individual species histories in the Peninsula. To date most studies focus on geographical range dynamics during the Pleistocene, but an increasing body of evidence shows that some species have also retained the genetic imprints of much more ancient processes. Many widespread Iberian species show a deep and often remarkably clear-cut divide between populations from the Mediterranean and from the Atlantic regions of the Iberian Peninsula, suggesting that both areas have independently sustained viable populations over extended periods. In fact, phylogeographical studies commonly find that species had several glacial refugia across the Iberian Peninsula. On the other hand, distribution models help identifying further suitable areas that could have sustained so far undetected refugia. Such studies are of interest for species conservation, because refugium populations are high-priority targets due to their long-term persistence and unique evolutionary trajectory. Overall, we conclude that palaeoecology, phylogeography and species distribution modelling have a great potential to inform each other because of their complementary perspectives and results. A true integration of these approaches is therefore fundamental for further progress in our understanding of past Iberian environments and the organisms they harboured.     

Microorganisms, mineral surfaces, and aquatic environments: learning from the past for future progress

The interactions between the geosphere and the biosphere are central questions in environmental and geological research. The relationship between bacteria and their environment is an important example of these interactions. By studying microbial communities in modern environments, it is possible to understand the underlying mechanisms that shape these environments and apply this knowledge to the rock record. Recently, new experimental and theoretical methods, ranging from nano- and biotechnology to mathematical and conceptual modelling, have come into play. Thus, new opportunities for interdisciplinary research in the field of geobiology have emerged. In this paper, we review aspects of state-of-the-art imaging and modelling techniques and propose a research concept linking the experimental and the theoretical approaches.     

A novel method for targeting survey effort to identify new bat roosts using habitat suitability modelling

In the UK, four out of 18 bat species are listed on the EU Habitats Directive, including the lesser horseshoe bat (Rhinolophus hipposideros), and their population status is closely monitored by visiting known roosts. R. hipposideros predominantly form maternity roosts in buildings, but roosts are impermanent features in the landscape and their distribution changes as bats form new roosts and abandon others. Locating new roosts requires intensive surveys which are challenging and inefficient. In this study, we provide a novel model-based strategy to identify potential R. hipposideros maternity roost sites that can be used to monitor bat populations. First, we model potential maternity roost habitat using record centre data on roost locations across Wales, Great Britain. We then constrain the area identified from modelling using record centre data on locations of bats in areas with no known roosts. We used two variable selection methods and three pseudo-absence data sets (random background points, random points in buildings and target group selection of mammal records) to produce six habitat suitability models. The three pseudo-absence data sets produced different habitat suitability maps, demonstrating the influence of pseudo-absence selection on species distribution models. The six models were combined using weighted mean average to produce an ensemble model that performed better than individual models and that indicated high levels of congruence in areas predicted to have high habitat suitability for maternity roosts. Our model revealed an extensive area (6523 km²; 31% of the area of Wales) containing 18,051 buildings in suitable habitat. Using record centre data on bat activity outside commuting range from known roosts reduced the potential survey area to 133 km² (0.6% of the area of Wales) and 207 buildings. Our modelling outputs can be used to direct volunteers and bat surveyors in more targeted and efficient searches.     

Skeletal biology,functional asymmetry and the origins of "Handedness"

The past decade has witnessed the (re)emergence of a debate as to whether handedness is apomorphic within hominins. There are both qualitative and quantitative arguments, some which draw non-human primates into the handed sphere and others which exclude them. Ultimate questions concern origins of structural asymmetry of both brain and body and lateralized behaviours with implications for tool use and language. Lateralization is thus an important realm of phylogenetic study, and archaeologists and psychologists alike have sought to identify handedness within material culture. However, hand preference for tool manufacture and use among extant non-human primates, such as Cebus and Pan, suggests that the archaeological record may well be mute regarding the origins of laterality. In this paper, an argument is put forward positioning skeletal biology as a viable approach to the handedness origins issue. Behaviour is a mediator of the complementary processes of geometric modelling (change in size and shape) and histological remodelling (disuse osteopenia; microfracture repair); therefore, directional asymmetry in the pattern of skeletal modelling and remodelling is a putative signal of lateralized activity.     

A dynamic global equilibrium in carnivoran diversification over 20 million years

The ecological and evolutionary processes leading to present-day biological diversity can be inferred by reconstructing the phylogeny of living organisms, and then modelling potential processes that could have produced this genealogy. A more direct approach is to estimate past processes from the fossil record. The Carnivora (Mammalia) has both substantial extant species richness and a rich fossil record. We compiled species-level data for over 10 000 fossil occurrences of nearly 1400 carnivoran species. Using this compilation, we estimated extinction, speciation and net diversification for carnivorans through the Neogene (22–2 Ma), while simultaneously modelling sampling probability. Our analyses show that caniforms (dogs, bears and relatives) have higher speciation and extinction rates than feliforms (cats, hyenas and relatives), but lower rates of net diversification. We also find that despite continual species turnover, net carnivoran diversification through the Neogene is surprisingly stable, suggesting a saturated adaptive zone, despite restructuring of the physical environment. This result is strikingly different from analyses of carnivoran diversification estimated from extant species alone. Two intervals show elevated diversification rates (13–12 Ma and 4–3 Ma), although the precise causal factors behind the two peaks in carnivoran diversification remain open questions.     

Evaluating the predicted extinction risk of living amphibian species with the fossil record

Bridging the gap between the fossil record and conservation biology has recently become of great interest. The enormous number of documented extinctions across different taxa can provide insights into the extinction risk of living species. However, few studies have explored this connection. We used generalised boosted modelling to analyse the impact of several traits that are assumed to influence extinction risk on the stratigraphic duration of amphibian species in the fossil record. We used this fossil‐calibrated model to predict the extinction risk for living species. We observed a high consensus between our predicted species durations and the current IUCN Red List status of living amphibian species. We also found that today's Data Deficient species are mainly predicted to experience short durations, hinting at their likely high threat status. Our study suggests that the fossil record can be a suitable tool for the evaluation of current taxa‐specific Red Listing status.     

The fossil record and limb disparity of enantiornithines, the dominant flying birds of the Cretaceous

Morphometric and stratigraphic analyses that encompass the known fossil record of enantiornithine birds (Enantiornithes) are presented. These predominantly flighted taxa were the dominant birds of the second half of the Mesozoic; the enantiornithine lineage is known to have lasted for at least 60 million years (Ma), up until the end of the Cretaceous. Analyses of fossil record dynamics show that enantiornithine 'collectorship' since the 1980s approaches an exponential distribution, indicating that an asymptote in proportion of specimens has yet to be achieved. Data demonstrate that the fossil record of enantiornithines is complete enough for the extraction of biological patterns. Comparison of the available fossil specimens with a large data set of modern bird (Neornithes) limb proportions also illustrates that the known forelimb proportions of enantiornithines fall within the range of extant taxa; thus these birds likely encompassed the range of flight styles of extant birds. In contrast, most enantiornithines had hindlimb proportions that differ from any extant taxa. To explore this, ternary diagrams are used to graph enantiornithine limb variation and to identify some morphological oddities ( Otogornis , Gobipteryx ); taxa not directly comparable to modern birds. These exceptions are interesting – although anatomically uniform, and similar to extant avians in their wing proportions, some fossil enantiornithines likely had flight styles not seen among their living counterparts.     

Estimating past vegetation openness using pollen–vegetation relationships: A modelling approach

We used a modelling approach to assess past landscape openness in mid-Holocene natural vegetation. Two simple landscape scenarios were modelled: a first landscape was based on the “Vera cycle” hypothesis for western Europe, including different phases of herbivore-induced vegetation change and regeneration, while a second landscape was created based on views how a mid-Holocene natural vegetation may have looked like on the Swiss Plateau according to the closed canopy theory. These simulated landscapes were used to produce pollen assemblages by means of a pollen dispersal and deposition model. The resulting modelled pollen assemblages were then compared to a typical mid-Holocene pollen record from the Swiss Plateau. Our results indicated that the mid-Holocene pollen record is likely to be the result of a closed beech forest. However, the vegetation cover on the Swiss Plateau had components from both the closed woodland and the wood pasture landscape designs, with the latter likely at frequently disturbed or naturally open habitats.     

Evidence of Osedax worm borings in Pliocene (∼3 Ma) whale bone from the Mediterranean

Osedax worms subsist entirely on vertebrate skeletons on the seafloor, using root-like tissues to bore into and degrade the bones. Paleontologists have only recently begun to appreciate the possible destructive effect that these worms may have had on the marine vertebrate fossil record and little is known of their evolutionary history. Using microcomputed tomography, we document Osedax-like borings in a fossil whale bone from the Pliocene of Italy and present new data on the borings of extant Osedax worms. The fossil borings are distinguished from those of other known borers and identified as traces of Osedax activity based on diagnostic features. Our results suggest that it is necessary to isolate individual borings for the confident identification of Osedax traces. This is only the second paleogeographic occurrence of Osedax in the fossil record and indicates that by the Pliocene these worms had colonised a large portion of the world's oceans. This is the first evidence for Osedax in the Mediterranean, past or present, and suggests that more species await discovery in this region.     

Response of vegetation to climatic changes of different duration in the late neogene

The late Neogene climate is characterized both by a general cooling at middle and high latitudes and by short-term temperature oscillations that developed into the ice ages. The effect of these climatic forcings on vegetation is known in only a few cases where the fossil record is sufficiently long, closely sampled and well dated. These records are important in testing models of vegetational change and in demonstrating that present vegetation is a product of past climatic variability on different temporal scales.     

Fighting the good cause: meaning,purpose, difference,and choice

Concepts of cause, choice, and information are closely related. A cause is a choice that can be held responsible. It is a difference that makes a difference. Information about past causes and their effects is a valuable commodity because it can be used to guide future choices. Information about criteria of choice is generated by choosing a subset from an ensemble for ‘reasons’ and has meaning for an interpreter when it is used to achieve an end. Natural selection evolves interpreters with ends. Surviving genes embody a textual record of past choices that had favorable outcomes. Consultation of these archives guides current choices. Purposive choice is well-informed difference making.     

The shape of pterosaur evolution: evidence from the fossil record

Abstract Although pterosaurs are a well‐known lineage of Mesozoic flying reptiles, their fossil record and evolutionary dynamics have never been adequately quantified. On the basis of a comprehensive data set of fossil occurrences correlated with taxon‐specific limb measurements, we show that the geological ages of pterosaur specimens closely approximate hypothesized patterns of phylogenetic divergence. Although the fossil record has expanded greatly in recent years, collectorship still approximates a sigmoid curve over time as many more specimens (and thus taxa) still remain undiscovered, yet our data suggest that the pterosaur fossil record is unbiased by sites of exceptional preservation (lagerstätte). This is because as new species are discovered the number of known formations and sites yielding pterosaur fossils has also increased – this would not be expected if the bulk of the record came from just a few exceptional faunas. Pterosaur morphological diversification is, however, strongly age biased: rarefaction analysis shows that peaks of diversity occur in the Late Jurassic and Early Cretaceous correlated with periods of increased limb disparity. In this respect, pterosaurs appear unique amongst flying vertebrates in that their disparity seems to have peaked relatively late in clade history. Comparative analyses also show that there is little evidence that the evolutionary diversification of pterosaurs was in any way constrained by the appearance and radiation of birds.     

Impulse response functions of terrestrial carbon cycle models: method and application

To provide a common currency for model comparison, validation and manipulation, we suggest and describe the use of impulse response functions, a concept well-developed in other fields, but only partially developed for use in terrestrial carbon cycle modelling. In this paper, we describe the derivation of impulse response functions, and then examine (i) the dynamics of a simple five-box biosphere carbon model; (ii) the dynamics of the CASA biosphere model, a spatially explicit NPP and soil carbon biogeochemistry model; and (iii) various diagnostics of the two models, including the latitudinal distribution of mean age, mean residence time and turnover time. We also (i) deconvolve the past history of terrestrial NPP from an estimate of past carbon sequestration using a derived impulse response function to test the performance of impulse response functions during periods of historical climate change; (ii) convolve impulse response functions from both the simple five-box model and the CASA model against a historical record of atmospheric δ¹³C to estimate the size of the terrestrial ¹³C isotopic disequilibrium; and (iii) convolve the same impulse response functions against a historical record of atmospheric ¹⁴C to estimate the ¹⁴C content and isotopic disequilibrium of the terrestrial biosphere at the 1° × 1° scale. Given their utility in model comparison, and the fact that they facilitate a number of numerical calculations that are difficult to perform with the complex carbon turnover models from which they are derived, we strongly urge the inclusion of impulse response functions as a diagnostic of the perturbation response of terrestrial carbon cycle models.     

Composition and structure of microbial communities from stromatolites of Hamelin Pool in Shark Bay, Western Australia

Stromatolites, organosedimentary structures formed by microbial activity, are found throughout the geological record and are important markers of biological history. More conspicuous in the past, stromatolites occur today in a few shallow marine environments, including Hamelin Pool in Shark Bay, Western Australia. Hamelin Pool stromatolites often have been considered contemporary analogs to ancient stromatolites, yet little is known about the microbial communities that build them. We used DNA-based molecular phylogenetic methods that do not require cultivation to study the microbial diversity of an irregular stromatolite and of the surface and interior of a domal stromatolite. To identify the constituents of the stromatolite communities, small subunit rRNA genes were amplified by PCR from community genomic DNA with universal primers, cloned, sequenced, and compared to known rRNA genes. The communities were highly diverse and novel. The average sequence identity of Hamelin Pool sequences compared to the >200,000 known rRNA sequences was only approximately 92%. Clone libraries were approximately 90% bacterial and approximately 10% archaeal, and eucaryotic rRNA genes were not detected in the libraries. The most abundant sequences were representative of novel proteobacteria (approximately 28%), planctomycetes ( approximately 17%), and actinobacteria (approximately 14%). Sequences representative of cyanobacteria, long considered to dominate these communities, comprised <5% of clones. Approximately 10% of the sequences were most closely related to those of alpha-proteobacterial anoxygenic phototrophs. These results provide a framework for understanding the kinds of organisms that build contemporary stromatolites, their ecology, and their relevance to stromatolites preserved in the geological record.     

Composition and Structure of Microbial Communities from Stromatolites of Hamelin Pool in Shark Bay, Western Australia

Stromatolites, organosedimentary structures formed by microbial activity, are found throughout the geological record and are important markers of biological history. More conspicuous in the past, stromatolites occur today in a few shallow marine environments, including Hamelin Pool in Shark Bay, Western Australia. Hamelin Pool stromatolites often have been considered contemporary analogs to ancient stromatolites, yet little is known about the microbial communities that build them. We used DNA-based molecular phylogenetic methods that do not require cultivation to study the microbial diversity of an irregular stromatolite and of the surface and interior of a domal stromatolite. To identify the constituents of the stromatolite communities, small subunit rRNA genes were amplified by PCR from community genomic DNA with universal primers, cloned, sequenced, and compared to known rRNA genes. The communities were highly diverse and novel. The average sequence identity of Hamelin Pool sequences compared to the >200,000 known rRNA sequences was only ~92%. Clone libraries were ~90% bacterial and ~10% archaeal, and eucaryotic rRNA genes were not detected in the libraries. The most abundant sequences were representative of novel proteobacteria (~28%), planctomycetes (~17%), and actinobacteria (~14%). Sequences representative of cyanobacteria, long considered to dominate these communities, comprised <5% of clones. Approximately 10% of the sequences were most closely related to those of α-proteobacterial anoxygenic phototrophs. These results provide a framework for understanding the kinds of organisms that build contemporary stromatolites, their ecology, and their relevance to stromatolites preserved in the geological record.     

The evolutionary history of krill inferred from nuclear large subunit rDNA sequence analysis

Early events in the speciation history of krill (Malacostraca: Euphausiacea), an abundant group of extant pelagic crustaceans, were studied with slowly evolving nuclear DNA sequences (large subunit ribosomal DNA, 28S rDNA). Krill have no fossil record, so very little is known about their paleobiology. The timing of past speciation events in krill was estimated by comparing change in their 28S rDNA to change in the 28S rDNA of their close relatives that do have a fossil record. Relationships between krill genera were also studied by phylogenetic analysis of partial 28S rDNA sequences. The analyses estimated the time that the last common ancestor of the krill family Euphausiidae lived to be the lower Cretaceous about 130 million years ago (Mya). Two lineages of krill survived the end Cretaceous extinctions 65 Mya and the modern genera of krill were established before the end of the Palaeogene 23 Mya.     

A new assemblage of Cenozoic lungfishes (Dipnoi: Lepidosirenidae) from the late Oligocene Nsungwe Formation,Rukwa Rift Basin,southwestern Tanzania

Lungfish (Dipnoi) date back to the Devonian, and some fossil taxa as well as extant African lungfishes are known for their ability to aestivate, tolerating low-oxygen environments associated with seasonal drying. Extant lungfishes are separated into two families: Lepidosirenidae (Protopterus in Africa and Lepidosiren in South America) and Neoceratodontidae (Neocerotadus in Australia). African lungfishes were more geographically and phylogenetically diverse on the continent in the past than they are today, with only 5% of extinct taxa recorded from the sub-Saharan fossil record. Given the sparse record of Lepidosirenidae fossils from continental Africa, any new materials are important for understanding diversification of the clade. Here we describe new lungfish fossils cautiously referable to Protopterus annectens and Protopterus aethiopicus, which are strongly supported sister taxa based on the molecular phylogeny. Specimens were collected from the late Oligocene Nsungwe Formation in the Rukwa Rift Basin (RRB) of southwestern Tanzania. The late Oligocene Nsungwe Formation represents a sequence of continental rift-fill deposits of the Songwe sub-basin of the RRB and is subdivided into the lower Utengule and upper Songwe members. Recovery of such material from the Paleogene of Africa below the equator addresses a sizable gap in the lungfish fossil record. It also expands the Nsungwe Formation fauna that includes invertebrates, alestid fishes, ptychadenid anurans, snakes, and several clades of mammals, deepening paleoecological insights into the late Oligocene record of the continental African interior. At present, P. aethiopicus and P. dolloi have an extensive modern eastern African distribution associated with the rift lakes and a region where extant members of P. annectens are not presently known. Fossil specimens described herein document presence of the clade during Paleogene volcanic activity in the western branch of the Eastern African Rift System.